constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
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there is no package called ‘spatstat’ #75

Closed brianpenghe closed 3 years ago

brianpenghe commented 3 years ago

I did install.packages('SoupX') and then library(SoupX). But I got this error:

Error: package or namespace load failed for ‘SoupX’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘spatstat’
Traceback:

1. library(SoupX)
2. tryCatch({
 .     attr(package, "LibPath") <- which.lib.loc
 .     ns <- loadNamespace(package, lib.loc)
 .     env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
 . }, error = function(e) {
 .     P <- if (!is.null(cc <- conditionCall(e))) 
 .         paste(" in", deparse(cc)[1L])
 .     else ""
 .     msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
 .         sQuote(package), P, conditionMessage(e))
 .     if (logical.return) 
 .         message(paste("Error:", msg), domain = NA)
 .     else stop(msg, call. = FALSE, domain = NA)
 . })
3. tryCatchList(expr, classes, parentenv, handlers)
4. tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. value[[3L]](cond)
6. stop(msg, call. = FALSE, domain = NA)

I then did install.packages('spatstat') and restarted the kernel, but the error is still there. Any ideas?

constantAmateur commented 3 years ago

This looks like an issue specific to your set up. I don't have any particular guesses as to what might be causing the issue. Maybe try verifying that 'spatstat' installed correctly by running load(spatstat)?